City of Heavenly Fire
by kaylap1410
Summary: What happens to our favorite heroes as they reach the end of their stories? Will Jace and Clary make it out alive? Will Sebastian take over the world? Who will die? Read on...
1. Chapter 1

Prologue~

The Institute was in ruins. Rubble was on the floor and nothing but gray rock was visible. Jonathan mouth curved up into a smile. He never understood why they had to another London Institute one hundred miles away from this one. Shadowhunters were idiotic. They used this battle ground for a reminder of how Shadowhunters can fight through anything. It made him sick. Shadowhunters were never heroes, only people who are ignorant enough to believe they are better than everything else. He never thought of himself as one of them.

Jonathan's smile spread throughout his face as he lit the match, watching the flame burn for a moment before letting it go. The fire consumed the rubble, burning everything in sight. Shadowhunters would not end up on top this time. Mundanes no longer have the right to be protected. Jonathan laughed and kicked a necklace that laid in the rubble."I believe that was mine," a voice boomed out. There beyond the flames, was a young girl. Her smooth brown hair blew in the wind and her dark gray-brown eyes stared at him with calculation. Jonathan thought she had looked familiar, as if he had seen her a thousand times before. He reached for the cup for a quick second but quickly put it away.

"Warlock or Shadowhunter?" he smirked. She only shook her head.

"The demon part of you is extremely dominate to the Shadowhunter side. It doesn't make since to me, you know. I am half demon myself and yet I do not have dark heart as you do. Why do you feel connected to Lilith might I ask?"

"My parents always saw me as the dark little demon that I was," he muttered, smile smacked from his face.

"I clearly can't reason with you," she responded, "This is not my fight as much I wish otherwise. I made a promises the day these walls crumbled that I would not interfere with his history. He made me promise and I did. But I warn you now that as much as you wish it to be not true, the bad guys never win." With she last words she turned and walked away, her tall and slender height shrinking and her hair sifting colors. Jonathan blinked for a moment before picking up the necklace. He looked at it for a moment, seeing the shape of an angel melded in the bronze metal. Along the wings were gears and sprockets. Jonathan smiled to himself for a moment before throwing it into the fire, grabbing the dark powder, and walking away.

She was waiting for him just as he arrived on the dock. Her arms were curled up together and she had an irritated look on her face. Jonathan sighed, knowing this girl was about to yell at him for being late."Sebastian," she complained, using the name they started to call him after the latest war, "I have been waiting for you to come back for hours! You promised if I helped you get into London, you'd be quick."

"My dearest, Ariana Lovelace, I told you I'd get what you desire, did I not?" he responded to the girl. She smiled at him, throwing her arms around him.

"You found it? I knew I could trust you! Brother told me I would be idiotic to believe you would retrieve the necklace. That Tessa must have took it a long time ago. That I shouldn't believe your lies," she screech. Jonathan smiled, tightening his grip on the girl as she continued to laugh in his arms.

"My dearest Ariana, of course I found you necklace. But I don't believe you have anything more to offer me," he muttered. She stopped laughing and remained perfectly still then as he increased pressure on her hips.

"You threw it in the fire, didn't you?" she choked. She struggled to be released of his clutches but Jonathan continued to hold on. He was too strong for her and she couldn't fight him much longer.

"You know me all too well, sweetheart. But I can't have any loose ends now," he let go of her waist and moved his hand to her wrists as the other reached into his pocket. He pulled out the cup and smiled.

"You'll be brilliant," he whispered as he dunked the cup into the ocean and put it on her lips. He watched her drink it. Watched her expression change. It made him happy to know that he was one less Shadowhunter away from winning this battle. She fell to the floor and he picked her up placing her into the boat. It would be a long day, before he would reach his army but he knew the trip was worth it. He clutched the powder in his right hand, his finger tracing a small "M" in it. Within several moments, it will be the weapon that ensures his victory. No Shadowhunter could fight him, not even her. He thought of his little sister often now. Clary was nothing but a coward to him before their little road trip around Europe, but now Jonathan knew otherwise to underestimate her. She caught on quickly and if she figured out how to use her rune power to it's full capability...

Jonathan shook his head. She would not be his downfall. She had a weakness that he knew about. She cared too much. She would do anything for those whom she loved, including dying. Jonathan would prefer not killing his sister, the last of the Morgenstern's that he could still call family, but if there was no other option, he would happily drive his sword through her there was his adoptive brother, Jace. Though he insists that his adoptive family would be the Lightwoods, ignorant boy. Jonathan had no idea what his sister saw in him. The only thing that kept Jonathan from killing Jace was Valentine's love for his fake son. It was the love Jonathan, despite the fact he always excelled at everything he did, never received. Not only did his father love Jace more than him, but so did his sister. Their relationship made Jonathan want to throw up. Valentine had always told him, and most likely Jace as well, that to love was to destroy. Now he was running off with a bitchy redhead that only a few months ago he believed was his sister. It was sick.

He turned into the dock then. There sat her. Her blonde hair brew about in the wind along with her elegant black dress. Her red lips did not curve up when she saw Jonathan. She remained expressionless. Waiting until he jumped out of the boat, walked towards her, and kissed her. He kissed her hard and rough. There was no gentleness in their kiss. She broke apart first.

"Did you find the powder?" she questioned him. He smiled a cynical smile at her.

"Am I me?" he responded. She started to walk towards the boat.

"You make Lilith proud, you know," she waited at the edge of the boat, waiting for him to hand her the powder, "despite the fact that you killed the Gray Sister that would have done this for you without hassle. Now hand me the powder," she took the powder from his hands. She move her hands to shape a blade, the powder followed them and hardened to revile a dark sword.

"Now don't make us regret putting our faith in you, young Shadowhunter," she handed him the sword. He frowned at her, "I am not a Shadowhunter. I am not as ignorant as them."

"Yet your blood disagrees with you," and with that she took control of the boat.


	2. Chapter 2

**Disclaimer: I obviously don't own anything in this series. I have my own idea of how this series will end but I am most likely far off.**

**Thanks for the three reviews, favorite, and follows by the way. I was unsure I'd get any so quickly. But to the person who wanted me to change the title: I am aware the title is already taken. City of Heavenly Fire is the next book in the TMI series and this is what I think will happen in that book. But if you want me to change it so it's slightly different, I will... Thanks :)**

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Chapter One: A Long Two Weeks

Clary took one step forward, facing him, looking him down. Jace was trying so hard to not laugh, she could tell. She sighed.

"Jace, if you're not going to take this seriously anymore, I'll go ask Izzy," she complained. At that moment, Jace finally cracked and started laughing his ass off. Clary stood there with her hands on her hips waiting for him to finish. He ran to kiss his girlfriend but she pushed away from him. He reached out to grab her face.

"Clary, your hair is blue, you know that, right," he laughed, Clary frowned. It was his fault it was blue in the first place. He decided that he was going to boil Kool-Aid and leave it last minute as it exploded throughout the kitchen, drenching Clary in the blue dye. No matter how much she scrubbed it, she couldn't get it out.

"Yes, Jace. I am aware that my hair is blue. Maybe you could explain it to Sebastian when we fight in the war," she unclipped her seraph blade from her gear, "Jace, we don't have time for exploding Kool-Aid in the kitchen or laughing about blue hair," she complained, "I have to become an amazing Shadowhunter as soon as possible. Who knows when he will strike? In a few days the world could fall apart and we will all be dead!"

"I know, Clary!" Jace said as he quit laughing, "But can we have one moment where this isn't killing us inside? I love you, Clary. You and your blue hair. And if you want to train, I will train with you," he leaned in a kissed her.

"You're really good at acting innocent, you know," she muttered. He laughed at her as he ran to the other side of the room. She took a breath and took the blade into her hands.

"On your mark," Jace yelled as the targets set up. Clary took a deep lunge into the ground as she clutched the knife harder.

"Get set," Clary let out an exasperated sigh. The targets started to move.

"Go," Jace said. Clary jumped a threw her blade, knocking over a target. She smiled as she took out another blade. As she ran to retrieve the first, she threw the seraph blade at the second target, letting it soar before it buried itself in the hard wood. Clary turned to see a sword, longer than her arm, fly through the air, heading towards her. She ducked, falling to floor. As she rolled out of her fall, she threw her blade at the third and final target. She laughed with pleasure as her blade succeeded in knocking it over.

Then Clary sprinted straight to the wall, leaping, letting her hands grabbed the rocks on it. She took a moment to catch her balance before climbing upwards anymore. She would have to climb to the high ceiling before she could strap up for the next stage of the obstacle course. Clary never liked heights and knowing that the only thing keeping her from falling a nine foot drop to the floor now was her strength, frighten her more than took in a deep breathe and remained looking up. Only a couple more feet until she reached the platform above. She reached out. The next rock was much further than the others. She stretched out her hand and clasped as tight as she could. Quickly Clary pulled herself up onto the platform. She smiled, looking down.

The harness was bothersome but she had to master her flips. Within a matter of clips, Clary was strapped up in the rope and ready to jump. She took a quick look at Jace. He was looking at his watch now but she knew this was the section he was waiting for. He kept trying to perfect her flips all the time during training. Clary was getting better but she had yet done it without scream or messing up her form. She held her breath as she leapt, her heart sinking for a moment before she could tell herself that she wasn't going to die. She stopped screaming inside her head and focused on doing the perfect flip. The next thing she knew, she was bouncing back into the air ready to do another and another, until the bungee chord no longer bounced and Clary had stopped moving.

Jace laughed and yell at her, smile wider than the Grand Canyon. "Clary! You did it! Not only was that your best time but the flips were perfect! You were amazing!" Jace yelled as he unhooked her from the harness and fell on top of her. Clary beamed. She had finally done something right. Granted training was a lot easier now that she had first on experience but she could never do that obstacle coarse right before. She was a long way from being as good as Izzy or Jace but she was ready for more runes, today.

"I had a great teacher," she whispered and Jace leaned in to kiss her. He dug his face through her red hair, brushing out the curls. Clary loved it when Jace played with her hair. He was never too rough to hurt her but not too gentle like he could withhold his love for her. She grabbed him, bringing him closer to her to deepen the kiss, when Clary felt the sparks that meant the kiss was over. She pushed on his chest and he snapped up.

"Sorry," he whispered as he rolled off of her. At that moment they heard the click of heels coming from the hallway. Clary and Jace looked as the doors open and clicking of two women's heels came towards them.

"Clary," Maryse said in a formal, business-like demeanor, "this is your new trainer." Clary started at the girl. She had long blonde curly hair that reached her waist. Her dark blue eyes looked like the waves breaking in the ocean at night. The pigment seemed to flow throughout her eyes. They stared at Jace and Clary with intensity with evaluation. Her lips were full with bright red lipstick smothered on them that contrasted well with her light skin tone. She was in black gear that showed off her invisible waist and perfect hips. She wore high black platform shoes that completely She frowned. She didn't talk or doing anything. There was an awkward pause before Maryse stepped in once more.

"Her name is Makayla Heart. She is a very well respected Shadowhunter and the Clave choose the best to train you, Clary. They Clave is very invested in your training. They now believe you could be some help in capturing you brother," there was another pause as they remained silent. Jace extended his hand.

"Jace Lightwood," he said triumphantly. He smiled at her showing off his crooked teeth, "and this is my girlfriend, Clarissa. We've all collectively been training her. She didn't know she was a Shadowhunter until several months from now so she's behind. But she catches up quickly," he winked at her as Clary blushed. Jace was so perfect with everyone, sometimes it was hard just to be in the same room as him.

"I'm aware of her 'special situation' as Jocelyn and Valentine's daughter. The Clave wishes for me to bring out the natural talent that she must have been born with. And from the look of this room and her current hair color she needs as much help as possible," she snapped, clearly not falling for Jace's bubbly personality. Clary didn't no whether to be offended or excepting the fact that she wasn't a good Shadowhunter. Her mother never wanted her mixed up with the Clave or her father and lied to her for sixteen years by taking away her memories. So Clary hadn't started training until three months ago, after the War in Idris, the Shadowhunter country. It was frustrating when Jace could execute everything so perfectly and Clary was still in the beginner levels. Clary's fingers moved to her hair, "It wasn't my fault..." she whispered.

"Anyways," Makayla moved on, "I have much to do today so I recommend cleaning yourself off and getting ready for tomorrow. I will not have a student late. And keep your boyfriend on his leash. I'm not looking for any puppy dogs in my gym," with her last statement she left the gym and headed towards the rooms.

"What a bitch," Jace muttered, "this is who you pick to train Clary?"

"I didn't pick her, Jace. The Clave think she'll be a good person to train Clary. You can't be the protective boyfriend forever," Maryse told him.

"She totally ripped on her! I know Clary. I've seen what she can do. She is better than some Shadowhunters her age already! Plus what she can do with runes..." he cut himself off and turn to the bluish redhead, "you are much better than she knows, Claire."

Clary looked at him and frowned. "Jace, I think I've seen her before," she said.

"Well she has been at several of the Clave gatherings. It would make sense if you have," Maryse said. Clary still looked unconvinced but wasn't willing to question the Clave's authority after running off to save Jace without permission. They barely got out of that predicament without getting in trouble and she didn't need to burn any bridges if she didn't have to.

"Yeah," Clary responded, "it must have been from then." She grabbed Jace's hand and ran towards the door. Her regular clothes were in his bedroom, thrown across his bed. Clary held his hand the entire run to his room and now it was burning. She quickly let go of it and grabbed her clothes. Clary went into the bathroom and changed.

"Where have you seen her before, Clary?" Jace yelled through the door.

"I don't know! Look Jace. It's nothing, me being freaked out. I've been on edge lately waiting for Sebastian's next attack that any bitchy person I see freaks me out," she stepped out of the bathroom, "what is going to happen, Jace? We seriously just going to wait here for him to kill us all like the Clave says?"

"I told you, I'm looking into that. I just don't get it. It's been two weeks since Ireland, he would have had enough time to create a large army of demon Shadowhunters. He would have attacked by now," he sat on the bed and ran his hands through his golden blonde hair that was now in desperate need of a haircut. Clary moved and sat next to him.

"I've been thinking about that too. If Sebastian believed he would win the war without a doubt, he would have already been here."

"So?" he questioned her."So there must be something or someone he's afraid to fight if he isn't here. He has to be looking for something that will make him EVEN stronger," she took a breath and looked towards the ceiling. Jace put a comforting hand on her shoulder.

"We'll stop him, you now that. I've killed him once," Jace smiled."Yeah, well that was behind his back."

"So when I kill him this time, I make sure to flip him over first," Clary laughed and hit him in the head. He laid on his back and put his hands over his head."Thanks for reminding me how much of an asshat you are," Clary giggled.

"You really need to stop using the world asshat, Love." Jace pulled Clary close to him and kissed her, pressing his lips against hers with pressure so her lips part. Clary smiled. It seemed nowadays he was the only one that could make her laugh. She loved him more than anything. She wished she hadn't felt the spark that meant Jace would break away. She didn't want him to break away. She wanted to be with him, always. But of course he slide off of her.

"Have the Silent Brothers found anything? Any leads that could stop the fire?" Clary said breathlessly. Jace looked up.

"No. Nothing. And I feel like I'm going to punch my fist inside a wall every time I'm with you. Why do you have to be so irresistible?" Clary ignored his question knowing that answering it would only lead into more kissing.

"There has to be something. Is it still impossible to contact the angel? Why would he make the fire permeant?" Clary said frustrated. Jace sighed and put an arm around her.

"Maybe as a permeant reminder to never bring back the dead?" Clary blushed at Jace's comment.

"If I didn't you wouldn't be here right now and we wouldn't be having this issue. Plus you would have never seen me with blue hair," Clary smiled, grabbing the tips of blue. Jace smiled too?

"I'd be deprived. You look so sexy with blue hair," he laughed.

"Yeah and do you have any idea how to get it out. I really don't want to ride into battle with my hair dyed from Kool-Aid," she responded. Jace laughed and looked at her.

"You know I would do anything to protect you?" he said in a form of a question.

"What does that have to do with anything?" Clary asked.

"I just don't want you to get you hopes up if I..." he cut himself off.

"Jace, we'll be fine. We have each other and we can do anything together. You just have to trust me. Don't be saying stupid things like that," she responded. Jace smiled."I love you," he brushed her hair.

"So do I," she pecked his lips with hers and jumped off the bed. She reached out her hand for Jace to take it.

"Come on. I told my mom we'd be home for dinner. She may like you now she knows we can't... you know, but she HATES it when people are late," Clary said to him.

"Yeah, I know," he frowned. She laughed at him.

"Are you mad because we have a curfew or the fact my mom likes you now we can't have sex anytime soon?"

"What do you think?" he raised his eyebrow at her. She hit his arm.

"You pervert. When are you going to let it go and move on?

"I'm a teenage boy, woman! My hormones are going crazy all the time and it doesn't help when the girl I love wears black tank tops and tiny short shorts!" she laughed at his pain and brushed her hand across his face sexually. Before he could catch her, she started running down the hall.

"I hate you," he mumbled and he ran and grabbed her by her stomach. Clary laughed harder.

"Let me down!" she screamed as he threw her over his shoulder. At that moment, Alec walked out into the hall.

"Oh, sorry. I disrupted you guys," he snarked. Alec was in his pajamas with his hair all over the place. It looked as though he hadn't slept in ages. Jace put Clary down and she looked at her boyfriend questionably.

"Magnus broke up with him," Jace whispered in Clary's ear. It made a lot of sense. Clary had barley seen Alec for two weeks and the only time she had seen him was in the kitchen. He had grabbed a carton of ice cream and went back into his room.

"Oh, Alec. I...um...how are you...um..."

"You don't have to act awkward around me, Clary. I'll get over it. It wasn't like it would last forever. He's immortal and last time I check, I can die. By the way, he told me to keep you guys away from him. He said he wasn't willing to become the Shadowhunters monkey Warlock and apparently he has more important things to do than take care of my friends," Alec said miserably. Jace and Clary stood there awkwardly.

"Go ahead," Alec told them, "go be a happy couple. No need to make yourselves unhappy on my account. You were doing something right?"

"I need to go home for dinner and-" Alec cut her off.

"Jace is going with you? Have fun," he said trying to put a smile on his face but failed and continued frowning.

"Are you sure you're okay, Alec. If you need me to stay, I'm sure Clary would understand," Jace said. Clary nodded. If Alec needed his brother, she wasn't going to prevent Jace from helping him.

"No, I'm fine. Honestly. Go have fun," he shook them off. Before Jace or Clary could protest, he ran back inside his room.

"Come on, let's have dinner," Jace said not moving his eyes from Alec's door. Clary placed her hand in his and walked towards the elevator.


End file.
